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In both the House and Senate versions of the legislation, defense lawmakers have inserted $74 billion toward a number of weapons programs "those that have outlived their usefulness" to the department, Panetta said in a speech at the National Press Club in Washington.

"I expressed concerns about the [legislation], which needlessly divert $74 billion over the next decade into programs, equipment and activities we don’t want or need," the DOD chief said.

"As the final legislation is negotiated in conference, we are working with our partners in Congress to improve it," he added.

With the department staring down a potential $500 billion budget cut under the White House's sequestration plan, "we must make every dollar count," according to Panetta

That pressure has forced DOD to make some difficult decisions to maintain U.S. military readiness in the face of fiscal uncertainty. With that kind of margin for error, the Pentagon has no wiggle room to accommodate struggling programs that "have a natural political constituency," according Panetta.

But Panetta's argument may have fallen on deaf ears, according to a top Senate defense lawmaker.

Senate Armed Services Committee Chairman Carl Levin Carl Milton LevinListen, learn and lead: Congressional newcomers should leave the extremist tactics at home House Democrats poised to set a dangerous precedent with president’s tax returns The Hill's 12:30 Report — Sponsored by Delta Air Lines — White House to 'temporarily reinstate' Acosta's press pass after judge issues order | Graham to take over Judiciary panel | Hand recount for Florida Senate race MORE (D-Mich.) told reporters on Tuesday the final conference report of the defense bill was done, and pass both chambers by the end of the week.

Committee aides and lawmakers are staying tight-lipped on how the conference landed on contentious issues like indefinite detention, biofuels, cuts to the Air Guard and other weapons programs and several social issues. But those compromises should come to light Tuesday with the final committee report.